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Manganese in PDB 4ut3: X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide

Enzymatic activity of X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide

All present enzymatic activity of X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide:
3.1.3.16;

Protein crystallography data

The structure of X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide, PDB code: 4ut3 was solved by M.Zeh Silva, J.Kopec, D.Fotinou, R.A.Steiner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.40 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.450, 105.220, 89.820, 90.00, 90.34, 90.00
R / Rfree (%) 17.336 / 21.146

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide (pdb code 4ut3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide, PDB code: 4ut3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4ut3

Go back to Manganese Binding Sites List in 4ut3
Manganese binding site 1 out of 4 in the X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:33.1
occ:1.00
 O A:HOH2022 2.0 39.3 1.0
OD2 A:ASP64 2.0 32.2 1.0
O3 A:PO4501 2.0 44.4 1.0
OD2 A:ASP92 2.1 29.1 1.0
NE2 A:HIS66 2.2 27.6 1.0
O A:HOH2021 2.2 21.2 1.0
CG A:ASP92 3.1 27.1 1.0
CE1 A:HIS66 3.1 29.3 1.0
P A:PO4501 3.2 44.3 1.0
CG A:ASP64 3.2 35.5 1.0
CD2 A:HIS66 3.2 29.8 1.0
MN A:MN401 3.3 24.1 1.0
CB A:ASP92 3.5 29.7 1.0
O4 A:PO4501 3.6 39.6 1.0
O2 A:PO4501 3.8 47.2 1.0
O A:HOH2074 3.9 50.8 1.0
CB A:ASP64 4.0 36.2 1.0
OD1 A:ASP64 4.1 39.9 1.0
OD1 A:ASP92 4.1 26.0 1.0
NH1 A:ARG96 4.2 57.1 1.0
ND1 A:HIS66 4.3 29.4 1.0
O1 A:PO4501 4.3 49.0 1.0
CG A:HIS66 4.4 31.1 1.0
CD2 A:HIS125 4.4 36.2 1.0
OH A:TYR272 4.4 41.2 1.0
NE2 A:HIS125 4.5 35.0 1.0
O A:HIS248 4.5 36.0 1.0
NE2 A:HIS173 4.6 25.8 1.0
CE1 A:HIS173 4.6 28.3 1.0
CA A:HIS248 4.8 30.1 1.0
C A:HIS248 4.9 34.1 1.0
CE2 A:PHE267 4.9 39.9 1.0
OD1 A:ASN124 4.9 21.5 1.0
ND1 A:HIS248 5.0 25.9 1.0
CA A:ASP92 5.0 30.6 1.0

Manganese binding site 2 out of 4 in 4ut3

Go back to Manganese Binding Sites List in 4ut3
Manganese binding site 2 out of 4 in the X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:24.1
occ:1.00
 O A:HOH2021 1.8 21.2 1.0
OD1 A:ASN124 1.9 21.5 1.0
O4 A:PO4501 2.2 39.6 1.0
OD2 A:ASP92 2.2 29.1 1.0
NE2 A:HIS173 2.2 25.8 1.0
ND1 A:HIS248 2.3 25.9 1.0
CE1 A:HIS248 3.0 23.8 1.0
CG A:ASP92 3.0 27.1 1.0
CG A:ASN124 3.0 26.7 1.0
OD1 A:ASP92 3.2 26.0 1.0
CD2 A:HIS173 3.2 27.3 1.0
CE1 A:HIS173 3.2 28.3 1.0
P A:PO4501 3.3 44.3 1.0
MN A:MN400 3.3 33.1 1.0
CG A:HIS248 3.5 28.2 1.0
ND2 A:ASN124 3.5 26.8 1.0
O3 A:PO4501 3.6 44.4 1.0
CA A:HIS248 3.9 30.1 1.0
O2 A:PO4501 4.1 47.2 1.0
OD2 A:ASP64 4.1 32.2 1.0
CB A:HIS248 4.1 29.8 1.0
CD2 A:HIS125 4.2 36.2 1.0
NE2 A:HIS248 4.2 25.0 1.0
O A:HIS248 4.2 36.0 1.0
CB A:ASN124 4.3 28.2 1.0
ND1 A:HIS173 4.3 26.5 1.0
CB A:ASP92 4.4 29.7 1.0
CG A:HIS173 4.4 25.8 1.0
N A:ASN124 4.4 31.3 1.0
O1 A:PO4501 4.4 49.0 1.0
CD2 A:HIS248 4.5 26.1 1.0
C A:HIS248 4.6 34.1 1.0
O A:LEU205 4.6 31.5 1.0
NE2 A:HIS125 4.8 35.0 1.0
CA A:ASN124 4.8 29.8 1.0
N A:HIS248 4.9 28.5 1.0
O A:HOH2022 4.9 39.3 1.0
CG A:ASP64 5.0 35.5 1.0

Manganese binding site 3 out of 4 in 4ut3

Go back to Manganese Binding Sites List in 4ut3
Manganese binding site 3 out of 4 in the X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn400

b:35.2
occ:1.00
 OD2 B:ASP64 2.0 36.6 1.0
OD2 B:ASP92 2.0 31.2 1.0
O B:HOH2018 2.1 47.9 1.0
O B:HOH2017 2.2 33.4 1.0
O3 B:PO4501 2.2 41.2 1.0
NE2 B:HIS66 2.3 30.7 1.0
CG B:ASP92 3.1 30.1 1.0
CE1 B:HIS66 3.2 32.7 1.0
CG B:ASP64 3.2 38.5 1.0
P B:PO4501 3.2 48.8 1.0
CD2 B:HIS66 3.3 33.8 1.0
MN B:MN401 3.3 30.6 1.0
O1 B:PO4501 3.4 46.6 1.0
CB B:ASP92 3.5 35.0 1.0
O4 B:PO4501 3.9 44.0 1.0
CB B:ASP64 4.1 39.0 1.0
OD1 B:ASP64 4.1 38.6 1.0
OD1 B:ASP92 4.1 27.1 1.0
O B:HOH2064 4.2 58.0 1.0
NH1 B:ARG96 4.2 55.7 1.0
ND1 B:HIS66 4.3 32.2 1.0
CD2 B:HIS125 4.3 41.4 1.0
CG B:HIS66 4.4 32.2 1.0
OH B:TYR272 4.4 46.8 1.0
NE2 B:HIS125 4.4 40.4 1.0
O2 B:PO4501 4.5 49.4 1.0
O B:HIS248 4.5 39.4 1.0
NE2 B:HIS173 4.5 26.2 1.0
CE1 B:HIS173 4.6 29.5 1.0
CA B:HIS248 4.8 32.0 1.0
OD1 B:ASN124 4.8 31.9 1.0
C B:HIS248 4.9 33.9 1.0
CE2 B:PHE267 4.9 38.0 1.0
ND1 B:HIS248 4.9 27.4 1.0
CA B:ASP92 5.0 35.5 1.0

Manganese binding site 4 out of 4 in 4ut3

Go back to Manganese Binding Sites List in 4ut3
Manganese binding site 4 out of 4 in the X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of the Human PP1 Gamma Catalytic Subunit Treated with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:30.6
occ:1.00
 O B:HOH2017 1.8 33.4 1.0
OD1 B:ASN124 1.9 31.9 1.0
NE2 B:HIS173 2.1 26.2 1.0
O1 B:PO4501 2.2 46.6 1.0
OD2 B:ASP92 2.2 31.2 1.0
ND1 B:HIS248 2.3 27.4 1.0
CE1 B:HIS248 3.0 26.7 1.0
CG B:ASP92 3.0 30.1 1.0
CG B:ASN124 3.1 31.6 1.0
CE1 B:HIS173 3.1 29.5 1.0
CD2 B:HIS173 3.1 30.2 1.0
OD1 B:ASP92 3.2 27.1 1.0
MN B:MN400 3.3 35.2 1.0
P B:PO4501 3.5 48.8 1.0
CG B:HIS248 3.5 28.9 1.0
ND2 B:ASN124 3.6 34.5 1.0
O3 B:PO4501 3.8 41.2 1.0
CA B:HIS248 3.8 32.0 1.0
CB B:HIS248 4.0 28.7 1.0
OD2 B:ASP64 4.1 36.6 1.0
O4 B:PO4501 4.2 44.0 1.0
NE2 B:HIS248 4.2 25.9 1.0
O B:HIS248 4.2 39.4 1.0
ND1 B:HIS173 4.2 28.1 1.0
CD2 B:HIS125 4.3 41.4 1.0
CG B:HIS173 4.3 27.7 1.0
CB B:ASN124 4.3 32.5 1.0
CB B:ASP92 4.3 35.0 1.0
N B:ASN124 4.4 31.3 1.0
CD2 B:HIS248 4.5 28.2 1.0
O2 B:PO4501 4.5 49.4 1.0
C B:HIS248 4.5 33.9 1.0
O B:LEU205 4.6 30.8 1.0
N B:HIS248 4.8 29.4 1.0
O B:HOH2018 4.8 47.9 1.0
NE2 B:HIS125 4.9 40.4 1.0
CA B:ASN124 4.9 33.1 1.0
CG B:ASP64 4.9 38.5 1.0

Reference:

C.X.Santos, A.D.Hafstad, M.Beretta, M.Zhang, C.Molenaar, J.Kopec, D.Fotinou, T.V.Murray, A.M.Cobb, D.Martin, M.Zeh Silva, N.Anilkumar, K.Schroder, C.M.Shanahan, A.C.Brewer, R.P.Brandes, E.Blanc, M.Parsons, V.Belousov, R.Cammack, R.C.Hider, R.A.Steiner, A.M.Shah. Targeted Redox Inhibition of Protein Phosphatase 1 By NOX4 Regulates EIF2ALPHA-Mediated Stress Signaling. Embo J. V. 35 319 2016.
ISSN: ISSN 0261-4189
PubMed: 26742780
DOI: 10.15252/EMBJ.201592394
Page generated: Sat Oct 5 21:25:57 2024

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